If you're using Compiz/Unity, you can do this from the infamous CompizConfig Settings Manager, but it's a bit tricky.

The "Decoration Match" key in the Window Decoration plugin specifies the windows that do have decorations. To selectively disable window decorations you have to construct an expression that matches every window except the ones you want to disable.

For example, if you want to disable window decorations for windows whose titles end in "Mozilla Firefox" or "Chromium", you can set the decoration match to:

(!title=Mozilla Firefox$) & (!title=Chromium$)

Complete documentation for Compiz window matching is at http://wiki.compiz.org/WindowMatching